☰ Navigation Tabs
Bacterial beta-glucosidase reveals the structural and functional basis of genetic defects in human glucocerebrosidase 2 (GBA2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVU PDB ENTRY 5BVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PROPANE, PH 8, 15 % W/V PEG 6000.
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.974 α = 90 b = 187.974 β = 90 c = 99.075 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS PIXEL 2014-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.6 45.1 100 0.11 15.9 10.3 61406 1.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 100 1.32 1.7 10.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5BVU 2.6 162.61 58306 3081 99.97 0.20862 0.20559 0.2134 0.26649 0.2697 RANDOM 58.022
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.54 -0.27 -0.54 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.929 r_dihedral_angle_4_deg 17.16 r_dihedral_angle_3_deg 15.838 r_long_range_B_refined 8.36 r_long_range_B_other 8.354 r_dihedral_angle_1_deg 7.054 r_mcangle_it 6.594 r_mcangle_other 6.593 r_scangle_other 6.235 r_mcbond_it 4.476
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.929 r_dihedral_angle_4_deg 17.16 r_dihedral_angle_3_deg 15.838 r_long_range_B_refined 8.36 r_long_range_B_other 8.354 r_dihedral_angle_1_deg 7.054 r_mcangle_it 6.594 r_mcangle_other 6.593 r_scangle_other 6.235 r_mcbond_it 4.476 r_mcbond_other 4.475 r_scbond_it 4.208 r_scbond_other 4.208 r_angle_refined_deg 1.561 r_angle_other_deg 1.021 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11055 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing